<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hmm, it seems that you have the Model Panel set to autostart in your preferences. Now, Chimera probably should ignore autostarting tools when it is in nogui mode, but currently it doesn't. So what you will have to do for now (until we fix this) is to start Chimera normally, turn off the autostart of the Model Panel (and any other graphical tools probably), save the new preferences, and then run your script.<div><br></div><div>If you look in the "Preferences" preference category, it will show the location of the preferences file. You could squirrel away your original preferences file somewhere, make the version with no autostarting, copy <i>that</i> somewhere, and then put your original version back. You would then be able to use the no-autostarting preferences by specifying it's location with the --preferences startup option.<br><div><br></div><div>--Eric </div><div><br></div><div><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><br class="Apple-interchange-newline"></div></span></div><div><div>On Mar 8, 2010, at 7:32 PM, Sumitro Harjanto wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div lang="EN-SG" link="blue" vlink="blue" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><o:smarttagtype namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PersonName"><div class="Section1"><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Hi Eric,<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Thanks for the suggestion. I don’t really script, I usually use a c++ code / excel to generate the command (.cmd) files. Should be okay for the automation for now, if I run into any problem then I will post it up here again. =]<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> <o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Mean while I try running the command “chimera.exe –nogui” in PATH/chimera/bin but got the following error message. I followed the instruction and copy over the debug message (below). any advise? I’m on a win7 X86 platform btw.<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Thanks,<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Sumitro<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">-----------------------------------------------------------------------------------------------------<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Chimera failed abnormally; the exit code was: 1</span></font><font size="2" color="navy" face="Arial"><span lang="EN-GB" style="font-size: 10pt; font-family: Arial; color: navy; "><o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Use –debug command line option for the full error message.<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">--------------------------------------------------------------------------------------------------<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Cannot execute 'gzip': no automatic decompression of .Z files<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Traceback (most recent call last):<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\__main__.py", line 65, in <module><o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> value = chimeraInit.init(sys.argv)<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimeraInit.py", line 401, in init<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> extension.startup(startExtensions)<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\extension\base.py", line 1056, in startup<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> manager.autostartTools(extNames)<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\extension\base.py", line 959, in autostartTools<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> emo.activate()<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\ModelPanel\ChimeraExtension.py", line 23, in activate<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> display(self.module('base').ModelPanel.name)<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\dialogs.py", line 77, in display<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> dialog = find(name, create=1)<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\dialogs.py", line 62, in find<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> return d()<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\baseDialog.py", line 523, in __init__<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> BaseDialog.__init__(self, master, *args, **kw)<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\baseDialog.py", line 244, in __init__<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> self.fillInUI(self.__top)<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\ModelPanel\base.py", line 217, in fillInUI<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> self._addColumns()<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\ModelPanel\base.py", line 436, in _addColumns<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> self._buildTable()<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\ModelPanel\base.py", line 454, in _buildTable<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> % len(filter(lambda s: s == 1, self.shownColumns)))<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 1306, in __init__<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> cnf, kw)<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 307, in __init__<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> self.tk.call(widgetName, self._w, *extra)<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">_tkinter.TclError: invalid command name "tixScrolledHList"<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Return code: 1<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Press return or enter to to exit<o:p></o:p></span></font></div><div style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; margin-top: 0cm; margin-bottom: 0.0001pt; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div><div class="MsoNormal" align="center" style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; text-align: center; "><font size="3" face="Times New Roman"><span lang="EN-US" style="font-size: 12pt; "></span></font></div></div></div></o:smarttagtype></div></span></blockquote></div></div><br></div></body></html>